Is BCORL1 p.Ala74fs (c.220del) pathogenic?

BCORL1 p.Ala74fs (c.220del) is classified Uncertain significance in BCORL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-03-02). Absent from gnomAD v4.1.

How common is BCORL1 p.Ala74fs (c.220del) in the general population?

BCORL1 p.Ala74fs (c.220del) is absent from gnomAD v4.1 (gnomAD).

BCORL1 p.Ala74fs

c.220del · rs779498199 · VCV420626

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,202,286)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.9	GERP 1.6, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,202,286). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BCORL1
Protein: p.Ala74fs
Coding: c.220del
MANE Select: NM_001379451
dbSNP: rs779498199
Type: Deletion
Location: chrX:130012987 (GRCh38)
Structure: AlphaFold pLDDT 38.79 · 2 PDB
Residue 74: the 'disordered' region

Full BCORL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BCORL1 p.Asp1360_Leu1361delinsVal Uncertain significance ★★ same type
BCORL1 p.Leu521fs Likely pathogenic ★ same type
BCORL1 c.86+4del Uncertain significance ★ same type
BCORL1 p.Ala1646fs Uncertain significance ★ same type
BCORL1 p.Arg1334fs Uncertain significance ★ same type
BCORL1 p.Asn104del Uncertain significance ★ same type
BCORL1 p.Gln856fs Uncertain significance ★ same type
BCORL1 p.Glu1036fs Uncertain significance ★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bcorl1-p-ala74fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown